Transcription in Eukaryotes Molecular Biology

Exam 2

How many types of RNAPs are in eukaryotes?

three types, Pol I, Pol II and Pol III

What types of RNA molecules are transcribed by pol II?

mRNAs and non-coding RNAs

What is the structural organization of the Pol II?

made of multisubunits; the largest two subunits contain a cleft that holds the DNA and harbor the basic catalytic elements for addition of nucleotides and translocation. Some subunits interact with other regulatory proteins

What is the C-terminal domain (CTD)?

A part of Rpb1, the largest subunit of Pol II, that contains numerous repeats of a heptapeptide sequence

What do modifications to the CTD do?

plays a role in transcription process and RNA
processing

What is the Pol II core promoter?

the DNA sequence(s) around the transcription start site that binds general transcription factors which in turn recruit the polymerase, and directs the initiation of transcription

What are the two major types of promoters in eukaryotes?

Focused and dispersed

What are three examples of core promoter motifs (elements) for Pol II transcription?

TATA box, initiator elements (Inr), motif 10 elements (MTE), downstream promoter elements (DPE), upstream and downstream TFIIB recognition elements (BRE)

Do all the promoter elements appear in all promoters for Pol II transcription?

no, only a subset of them are found in each promoter, and they work together to control
gene transcription

What is the super core promoter?

the strongest existing promoter that contains optimized versions of TATA, Inr, MTE and DPE and has a very high affinity for TFIID

Are all TFIID the same?

No. They all share TBP and six core subunits, but differ in the number and combination of TAFs

Functions of TFIID

first to bind to the core promoter to initiate formation of pre-initiation complex, co-activates transcription

Functions of TFIIB

stabilizes TFIID binding to the core promoter, aids in recruiting TFIIF/Pol II

Functions of TFIIE

helps to recruit TFIIH, promotes promoter melting;

Functions of TFIIF

forms a tight complex with Pol II to enhance the polymerase’s affinity for the promoter/TFIID/TFIIB complex, aids in TSS selection and promoter
escape, enhances elongation efficiency

Functions of TFIIH

has helicase and kinase activities, crucial for promoter opening and clearance; kinase phosphorylates Ser5 of CTD, critical for
transition from initiation to elongation

What is the minimal pre-initiation complex (PIC)?

A complex of TFs associated with promoter DNA and the RNAP that is needed for transcription initiation

What is Mediator?

A large protein complex that work with PIC for the control of transcription initiation, allows the PIC to respond to regulating elements on
the genome at some distance from the promoter

What are the sequence of events of Pol II mediated transcription initiation?

1. activator binding to distal enhancer and mediator binds to the activator. 2. More activator binding to the mediator to alter its conformation. 3. TFIID binds to the core promoter, supported
by TIIB. 4. Pol II/TFIIF are recruited to the promoter/TFIID/TFIIB complex. 5. TFIIE and
TFIIH join the complex, and initiation starts

How is transcription terminated in Pol II-mediated transcription?

a polyadenylation signal AAUAAA located 3’ to the stop codon is recognized and bound by a cleavage and polyadenylation stimulating (or specificity) factor (CPSF). This factor recruits an
endonuclease to cut the transcript

What is the only type of RNA genes that Pol I transcribes?

rRNA genes

What does HMG stand for?

high-mobility group protein; HMG boxes are present in many DNA-binding proteins that bind DNA either sequence-specifically or
nonspecifically

What is enhanceosome?

a highly specific architecture that is crucial for recruiting TBP in Pol I transcription. it is formed by a complex of upstream binding factor, UBF, and DNA via UBF binding to upstream control element, UCE, and core promoter element

What is the major feature of the type 1 and type 2 promoters in Pol III transcribed genes?

both have promoter elements located within the body of the genes

What types of genes does pol III transcribe?

small genes including 5S rRNA gene,
tRNA genes, small nuclear RNAs of the spliceosome

What are the two major characteristics of transcription in eukaryotes we discussed?

transcription is pervasive with many species of RNAs produced, in addition to mRNAs; protein-coding genes account for only a small fraction of the genome

What does lncRNAs stand for?

long noncoding RNAs

What are the major functions of lncRNAs?

affect transcription, mRNA splicing, RNA processing, translation, protein localization, and formation of RNA-protein complexes

What are transcription factories?

regions in eukaryotic nucleus that transcription occur

What are the main components of a transcription factory?

RNAPs, general and specific TFs binding to promoters and enhancers

What does 4C technology stand for?

chromatin conformation capture-on-chip

What is 4C technology used for?

studying interactions between a particular genomic
locus with other loci in the genome, either on the same chromosome or on other chromosomes